That’s a giant squid (Architeuthis sp.) and at 3m long it’s a baby, full grown females can reach 13m. Giant squids are really deep sea predators, so beachings are relatively rare. This one appears to have been in a fight. We don’t know too much about the food webs at the bottom of the ocean, sperm whales are the only creatures known to take on adult giant squids but sharks and other whales might very well attack sub adults like this one. As an aside, studying parasites might be the best way to work out who eats who in the deeps. When you dissect a shark or a whale its stomach contents give you a picture of what it’s eaten recently, when you look at its parasites you can paint a picture of what it’s eaten over its lifetime. However the squid got its injuries, they proved fatal. it washed up dead and was returned to the ocean with the next high tide.

Then there was the announcement of the results of the Census of Marine Life, an inventory of the species living in the earth’s oceans. The news of that story was almost universally illustrated with pretty pictures of weird animals photographed from deep sea submersibles. Here’s a particularly striking example of the genre, an amphipod with a house which showed up in the Guardian and National Geographic:

Photo from Texas A&M press

Obviously, that mean-looking shrimp-like amphipod is a spineles creature, but it might suprise you that its transluscent home is also an animal. In fact, it’s one of your closest relatives in the biological world. It’s a salp, a relative of the sea squirts, and it’s a member of the chordata – the same phylum as the all the vertebrates. Matt Cobb has all the details in his guest post at why Evolution is True.

Finally, scientists published the first complete genome sequence from a sponge. As has become customary for genome studies, the press releases and the resulting new stories all suggest that these DNA sequences will help us fight cancer. Well, perhaps. Cancer is ultimately about uncontrolled cell proliferation and sponges are the simplest animals to have to find a way of marshalling thousands of cells into a single body. But is that really the only reason we should be exciting about a tool that helps us to understand the origins of multicellularity, or being able to see where the precursors of the development programs that pattern the bodies of more complex animals came from? I’d like to think the average reader is just an excited by a little scientific awe as they are by some ill defined and far off medical benefit. (Before I sound too grumpy I should say that the press release from UC Santa Barbara was really very good, it’s just a shame some of those points didn’t get picked up in the reporting.)

I got a little bit starry eyed writing about the Neanderthal genome the other day. I chose to retrace the arc of scientific progress that links the initial description of Neanderthal man as something different than modern humans to the point reached last month, where we are able to tag some of those differences to a single gene. Most of the news stories about the Neanderthal genome focused not on the genes that made us different from them, but a small percentage of the genome that reinforced the continuity been them and us. Genetic evidence that Neanderthals interbred with the ancestors of some modern humans. The revelation of these ancient assignations has caused some quite sensible people to say some quite silly things about what species are and what Neanderthals were. So, perhaps I can compliment my slightly hazy earlier piece with a more hardheaded take on why Neanderthals remain a species unto themselves.

Let’s start with the evidence that Neanderthals interbred with the ancestors of modern humans. Modern humans (Homo sapiens) arose in Africa about two hundred thousand years ago, all modern human populations outside of Africa descend from a relatively small number of migrants who left that continent between eighty and fifty thousand years ago. When those migrants first left Africa and entered the Middle East they would have met other humans. The ancestors of the Neanderthal had moved out of Africa and established themselves in Europe and Central Asia thousands of years before. Until now we haven’t known which of the four ‘F’s (fighting, fleeing, feeding or reproduction) followed that first contact, the Neanderthal genome has given us a clue.

When you compare individual DNA bases that are variable within modern human genomes to the corresponding sequences in the Neanderthal genome you find that non-African sequences match the Neanderthal sequence slightly (but significantly) more often than African sequences do. It’s possible that this pattern is an artifact of our poor sampling of African genomic diversity (that observant nerd Christie does a good job of explaining how here) but for the sake of argument let’s take it for granted that his pattern is the result of ancient interbreeding. The authors of the paper describing the Neanderthal genome estimate people with no recent African ancestry inherited between one and four percent of their genome from Neanderthals. That number is the same for Papuan and East Asian populations as it is for Europeans despite Neanderthals having lived alongside Europeans for thousands of years, suggesting any interbreeding that contributed to modern human genomes was limited to that first period of contact.

This is where the problems start. Having heard the news that Neanderthals and some of our ancestors might have once swapped genes some people remember that nice easy test of species-status from high-school biology. Something like “if two animals can interbreed then they’re part the same species.” So, are we Neanderthals; or are Neanderthals us? No. In fact, the Neanderthal genome serves to highlight some the mistakes we commonly make when start trying to define species.

Biologists have spent a lot of time arguing about just what a species is and how can delimit species from the creatures that we study, too often we’ve forgotten that those are two different arguments. DeLene from Wild Muse has a thoughtful overview of some of the factors that contribute to the “species problem” in her review of Jody Hey’s book on the same topic. You should read her piece because the species problem really is a fascinating philosophical question, but I think most of the fights that erupt around competing definitions of species come from a failure to understand that defining species and organising critters into species are two different tasks. We’ve been studying speciation, the process by which new species arise, for a while now and we’ve developed a pretty good idea of how it works. Two populations stop interbreeding with each other, during that period of “reproductive isolation” genetic changes in one population can’t effect the other so natural selection and random changes (called genetic drift) change each population independently. Species are populations which are on independent evolutionary trajectories.

Reproductive isolation drives the independence that is at the heart of what species are, but it’s not the sine qua non of a species. James Mallet from University College London has made a special study of hybridisation, and he reckons 10% of animal species and a whopping 25% of plants interbreed with other species from time to time. As molecular tools have been applied to non-model organisms it’s become increasingly clear that the “species barrier” is more porous than we’d thought, and species can maintain their independence even in the face of the occasional injection of genes from other species.(If you’re interested in the wider question, I’ve written a bit on the species problem here. The short version is we should see competing “species concepts” as operational tools that might be used to help delimit species, but not as definitions).

Now, think about the results from Neanderthal genome. Most sequences in that genome are separated from their human counterpart by a split that happened over five hundred thousand years ago. There is pretty good evidence that Neanderthals and the ancestors of non-Africans interbred when they met each other in the Middle East about four hundred and fifty thousand years after that initial split. That gene flow had the potential to homogenise the two populations into one, but it didn’t. Each lineage maintained its identity. For the twenty or so thousand years that Neanderthals continued to exist they retained identifiable morphological traits. There are fossils in Europe that some argue show a mixture of characters, but any interbreeding in that continent left no mark on modern European genomes, which have no more Neanderthal DNA than Papuan and Chinese genomes do. At the same time, the authors didn’t detect any flow of modern human genes into Neanderthal genomes (so it’s not a case of of modern humans swamping Neanderthal populations and erasing any trace of genetic admixture in the process). The available evidence seems to point o Neanderthals and modern humans as separately evolving populations, and a little bit of gene flow between them wasn’t enough to upset that pattern.

I should stress, by saying H. neanderthalensis and H. sapiens are different species we aren’t saying very much about how different Neanderthals were from us. Species are not defined by a degree of difference, or an essence that was missing in Neanderthals but is present in us, they’re just another human population that was moving in a different direction (and eventually extinction). If some of us do have Neanderthal genes, then it only goes to show how fuzzy the line between our species and the rest of the biological world is.

Homo sapiens means “wise man”. Sometimes it’s hard to think that Linnaeus was right in honouring our species with that name. We’re the reason the earth is going through its sixth great extinction; people are still routinely killed for belonging the wrong race, religion or sexuality and the prospect of taking action on climate change makes a significant proportion of the population behave like children. So it’s nice to be reminded every now and again about the sorts things our species can do when we put our minds to it. I’ve been trying to find time to write a proper post about the Neanderthal genome, but here’s something to think about on a rainy Friday afternoon.

In 1857 an anatomist and a school teacher, Hermann Schaffhausen and Johann Fuhlrott, described a set of bones that had been discovered in a limestone quarry in what was then called the neanderthal region of Germany. Amazingly, the neanderthal region was named after Joachim Neander whose own name translates as “new man”. A new man was exactly what Schaffhausen and Fuhlrott saw in the bones that they described. They were at once human and something “other” Chief among the characters that set the neanderthal samples apart from modern humans was the thick brow ridge that we now think of as characteristic of primitive humans. Thanks to these differences the school teacher and the anatomist concluded that the neanderthal samples were human but something quite different than modern Europeans.

“Neanderthal Man” was the first pre-human fossil to be described. At the time science had no convincing mechanism by which species might change over time and no idea of how organisms passed on traits to their offspring. Within in a couple of years Darwin had published The Origin and Mendel his Experiments on Plant Hybridization(which was promptly ignored, and only cited three times in 30 years).In time scientists discovered more human fossils; Neanderthal man showed up all over Europe and took the name H. neanderthalensis, Euguen Dobois uncovered H. erectus in Asia and host of anthropologists have since added characters like the Turkana boy, H. habilis, Ardi and a whole cast of Australopithecines to our family tree.

Last month, scientists published a first draft of the Neanderthal genome. 60% of the genetic make up of species of human that has been extinct for thirty thousand years. Thanks to the work of all those scientists listed above, and countless others who go unremembered, we now have a pretty good idea about the genetic basis of the thick brow ridge that convinved Schaffhausen and Fuhlrott than neanderthal man something different than other humans. The Runx2 gene is in a region of the genome that has been selected for in the H. sapiens lineage. We know from the work of yet more scientists that Runx2 is one of the most important genes regulating bone growth in humans and is associated with malformations of the skull. It’s no great stretch to imagine that our species lost the brow ridge that that we associate with primitive humans thanks to changes in the expression pattern of Runx2.

It some ways that’s a trivial piece of information, we’ve known for a long time that most morphological change is likely due to changes in the expression pattern of development genes. But isn’t it wonderful to think that in the span of two human lifetimes we’ve moved from knowing nothing of our species’ history to the point that we are developing hypothesis on the molecular basis of the changes that made us different from the host of human species we’ve since discovered.

As I’ve said before there really is no such thing as the human genome. There are millions of differences between individual genomes and we are each born with about 150 new muations. In an age in which we can sequence assemble and analyse entire genomes in two years understanding the breadth of human genetic diversity is at last an achievable goal and if you want to understand human diversity then you need to look to where we came from. Trace any family tree back far enough and you will end up in Africa and, in fact, most of human history was played out entirely in that continent. Modern humans arose in Africa about 250 000 years ago and only spread out to Europe and the rest of the world in the last 60 000 years, displacing Homo erectus in the process. The migrants that founded the modern European, Asian and American populations would have carried with them only fraction of humanity’s genetic diversity when they left Africa but untill recently genomics has focused on those populations. Until last week the two African genome sequences available to researchers were both from Yoruban volunteers to the hapmap project. Although those sequences are very useful they represent only one tip in the deeply branching tree of humanity

Summary of human genetic diversity redrawn from Campbell and Tishkoff (2008) doi:10.1146/annurev.genom.9.081307.164258 . Numbers in brackets are the number of complete genome sequences from each region available before last week.

To broaden our understanding of African genomes Schuster et al looked to the South of the continent and at two people in particular. !Gubi is a Khoisan (or bushman), a member of a one of the earliest diverging groups within the humanity while Desmond Tutu hails for various Bantu peoples. The results taken from theses genomes along with lower density sequencing and genotyping of other Bantu and Khoisan volunteers reinforces just how much genetic diversity exists within Afirca. By using a method called principle component analysis to reduce a the correlations among millions of single base pair differences (single nucleotide polymorphisms or SNPs) to a smaller set of uncorrelated vectors you can see patterns in the genetic diversity of groups. Applying this method to West African (Bantu and Yoruba), Khoisan and European populations reveals the comparative genetic homogeneity within Europeans and that the difference between the two African groups is comparable to that between either of them an Europeans.

All in all Schuster et al found 1.3 million SNPs that hadn’t been previously identified. Those new polymorphisms will be a boon to researchers searching for a genetic basis to, for instance, HIV restiance in Africa or African-American’s increased risk to type 2 diabetes. Just as interesting as the new SNPs is the discovery of others that have already been associated with diseases even though Desmond Tutu and !Gubi are healthy 80 year olds. A couple of scientists quoted in dispatches seem to think these genomes will act as quality control, allowing researchers to ‘clean up’ polymorphisms incorrectly associated with dieseases in other studies but it seems at least as likely that something more complex is going on. The selective, or health, value of a gene can only be measured against the environment it is expressed in and the rest of the genome is absolutely part of that environment. It’s entirely possible for a gene to be associated with Wolman disease amongst Europeans but to be of no consequence to busman thanks to the different genetic background against which it expressed.

Uncovering the genetic basis of these diseases and untangling the complex genetic interactions that underly populations’ risk to disease still lies in the future but this study also tells us something about our past. Most Khoisan are nomadic hunter-gathers and their ancestors have been for thousands of years, by comparing their sequences to those from agricultural societies you can see the evolutionary impacts of that change in lifestyle. Some malaria resistance genes, scars from humanities long battle with that disease that was amplified when agriculture lead to increased population density, are absent from the Khoisan sequences as are genes for digesting lactose as adults. Though those primitive characters have been retained by the Khoisan they are no more an ‘ancient’ or primitive people than the tuatara is a ‘living fossil’. In fact, there are a large number of bases in which European sequences are identical to the corresponding chimpanzee sequence while the Khoisan sequences diverge – lots of those changes will have been fixed at random but the fact some of them are in genes that are likely target of selection (especially perception of taste and smells and immune responses) suggests they may also have adaptive consequences.

There is something faintly pathetic about the Y-chromosome when its lined up with its peers in a karyotype. Each of the 22 numbered chromosomes pair off with a near identical partner just their size while the Y has to shape up to the X which has more than twice as much DNA and 25 times as many functional genes.

The puny Y-chromosome only looks worse when you realise that mammalian sex chromosomes weren’t always so mismatched. 160 million years ago the X and Y were just another pair of chromosomes, albeit the pair that the carried the sex determining gene SRY. Over time the chromosome that went on to become the Y stopped swapping genes with its partner, allowing it to maintain a suite of genes that are beneficial in male bodies but not in females. It’s the lack of genetic recombination that sent the Y into its decline. Genes on any other chromosome can be swaped between pairs, meaning over many generations individual gene copies (called alleles) are exposed to natural selection independently of alleles either side of them. The same process doesn’t apply to alleles on the Y-chromosome. Since the Y is always passed on as a single unit natural selection acts on the whole thing – a broken gene might make it into the next generation because it is attached to beneficial mutations. The efficiency of natural selection is further reduced in the Y-chromosome because it has a relatively small effective population size (less that one quarter of that for normal chromosomes since only males carry the Y and then in only one copy and even then a larger number of males than females don’t contribute to the next generation) which makes genetic drift a strong force.

What we’ve known about the Y-chromosome’s past has has shaped out ideas about what it is now and what it will become. Until quite recently the Y was seen as more or less a derelict chromosome, a few broken remnants of the genes still found on the X and a couple of male-specific genes hanging on the the sex determining gene SRY. People have even go so far as to extrapolate the Y’s long slow decline to a future time at which the Y will simply disappear. The first clue that the Y-chromosome might be a little more resilient than that came in 2003. The publication of the complete sequence of the human Y-chromosome revealed more than fossils from the Y’s more substantial ancestor. There are plenty of those so called “X-degenerate” segments but most of the active genes in the Y are in large repetitive runs of DNA called the “ampliconic regions”. The genes in these regions are mainly made of DNA sequences unique to the Y chromosome and are expressed only in the testes – suggesting the Y has been making its own genes at the same time that its been losing the X-degenerate ones.

Untill this week it has been hard to test the idea of a regenerating Y-chromosome in an evolutionary framework. Those large repeated runs of DNA are very hard to sequence (the standard metaphor is putting together a jigsaw puzzle made entirely of sky) so we haven’t had another Y-chromosome sequence to compare ours with. Now, thanks to Jeniffer Hughes and colleagues, we do and the result it stunning. Not only has the Y-chromosome been making genes, it’s been making them at an outrageous rate. Thirty percent of our Y-chromosome sequences have no counterpart in the chimpanzee. As the authors say that’s the sort of divergence you’d expect to see between humans and chickens, which are separated by 310 million years of evolution not humans and chimps which only split 6 million years ago!

It’s evident that, far from being in the tail end of an inexorable decline, the Y-chromosome is evolving a good deal more quickly than the rest of the genome. So, the burning question is what is behind that evolutionary rate? There is probably no single answer to that question but it’s safe to assume it results from some of the unique features of the Y-chromosome; a lack of genetic recombination, the presence of those large repetitive sections of DNA and the preponderance of male specific genes.

It’s usually a good idea when trying to explain an evolutionary phenomenon to think of explanations that don’t invoke natural selection as the main driver as a sort of null hypothesis against which to test other ideas. In this case the increased fixation of new genes on the Y-chromosome might simply reflect an increased rate of production of new genes. Those highly repetitive sections of the Y-chromosome are the perfect substrate for a process called ectopic gene conversion in which a Y-chromosome can recombine with itself and as a result duplicate streches of DNA. We know from human studies that a process like this has made wide scale structural changes in the last 100 000 years and it might be enough to explain the Y’s unusual gene production.

I think it’s very likely that natural selection also plays a role in the number of of those new genes that become fixed in the human and especially the chimp lineage. Most of the active genes on the Y-chromosome are expressed in the testes and involved in sperm production. Chimpanzees are highly polygynouspolygynandrous [Thanks to Harvest Bird for pulling me up on this,], in most cases a female will mate with each of several dominant males in a troop, and a result sperm competition is an important level of selection. Although humans aren’t as polygamous as chimps (and likely haven’t been in our recent history) it’s clear that fertility selection is still an important force and we know for sure that mutations in the Y-chromosome can lead to infertility so, again, the fate of new genes on the Y-chromosome are likely to be driven by selection.

Both the adaptive and non-adaptive explanations above might will be influenced by the lack of recombination in the Y-chromosome. The reduction in the efficiency of natural selection described above will stop very slightly deleterious mutations from being driven to extinction which might mean new genes that would be selected against on any other chromosome become fixed on the Y. This phenomenon can be enhanced when it is coupled with selection producing a ‘selective sweep’. If a new beneficial mutation, perhaps associated with sperm competition or fertitily selection, pops up in on a chromosome with a bunch of other mutations that whole thing will be selected for and driven to fixation which has the potential to make for large scale changes quickly.

It is likely that the amazing evolutionary rate of the Y-chromosome is a result of some combination of all these factors but it should be possible to disentangle at least some of their contributions. If sperm competition is a major driver of Y-chromosome evolution then it follows that animals that go in for purely monogamous relationships will have comparatively low rates. Evolution has furnished us a natural experiment to test this idea, all gibbon species form pair bonds and are highly monogamous. We could test the sperm production hypothesis by sequencing the Y-chromosome of two gibbon species and calculating the rate of evolution of a Y-chromosome in a monogamous species. .Although I’m happy to present the test of this idea I’m not going to line up to do it, those repetitive sections of DNA make sequencing Y-chromosome so hard that it took 13 years to do the human one and 8 to finish the chimp one.

When I started out as a genetics student the big goal everyone was talking about was understanding “The Genome” – that monolithic set of DNA bases that make us human. Of course, there is no such thing. Pick two human genomes at random and you’ll likely find 2 million single-base differences and plenty of structural differences on top of that. As with just about everything in life understanding the range of variation and the diversity in human genomes is much more interesting than focusing on the average of that diversity.

The publication of a draft sequence from the Human Genome Project in 2001 really was the begining of a new epoch in genetics (and a revelation in itself- it takes 20 000 genes to make a nematode and 25 000 to make us?) but the real value of that project has been the generation of a scaffold that subsequent projects like the super-optimistic 1000 genomes project, hapmap and the genographic project (which New Zealand researchers contribute to) have been able to inherit in their attempts to understand genomic diversity. This week Nature has a special issue focussing how data built on information from the Human Genome Project is contributing to the way we understand disease and even allowing personalised testing for genetic risk.

Unfortunately they’ve stuck one of the most interesting articles behind a pay wall (Nature, the people that bring you a special on science and society but don’t let society read it…) Bruce Lahn and Lanny Ebenstein have an opinion piece on genetics and race.

The current moral position is a sort of ‘biological egalitarianism’. … the view that no or almost no meaningful genetically based biological differences exist among human groups, with the exception of a few superficial traits such as skin colour. Proponents of this view seem to hope that, by promoting biological sameness, discrimination against groups or individuals will become groundless.

Of course, as Ebenstein and Lahn point out, there is a problem with this view – race almost certainly does have a genetic basis beyond a few superficial traits. To take the local slant Polynesians and in particular MÄori represent the furthest extent of the series of migrations that followed our ancestors moving out from Africa. Settling the Pacific must have involved a series of population bottlenecks – events in which small groups form a new population representing only a fraction of the genetic diversity in the parental population. Such bottlenecks will have inevitably left a mark on the gene pool of MÄori and Pacific Island populations that more recent interbreeding won’t yet have erased. There will be some genes that are unique to Polynesian populations and others that are orders of magnitude more or less common than they are in other populations. If we embrace that genetic diversity we might be able to understand why MÄori face a much greater risk to, for instance, diabetes, gout and liver disease than Pakeha. To, as people have really suggested, ignore that genetic diversity because racists might use it to further their stupid cause is, in the words of Lahn and Ebenstein “llogical, even dangerous”

Oh, and by the way, whatever we find out about the genetic basis of race I think it’s safe to say that genes won’t care too much for national borders – but that’s not going to stop the UK from genetically screening assylum seekers…

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